Dear Alex,
You might be interested by the tools at q4md-forcefieldtools.org.
Charge values are based on ab initio computations.
q4md-forcefieldtools contains programs you can install on your
machine(s), a database of FF libraries, a server/cluster to perform
what you need and tutorials.
regards, Francois
> Hi, my name is Alex and I want to clarify several moments I had noted
> during Antechamber procedure.
>
> Q1. How to prepare a correct molecule of the inhibitor?
> Adding all hydrogenes - it is OK thanks to chemaxon and openbabel.
>
> Q2. But what about the inital conformation (is it important or I can use
> plane structure?) and atom type assignation (for example in PO3 group I
> have to use O.co2 atom type, as it is mentioned in tripos mol2 manual or
> http://www.ccdc.cam.ac.uk/support/documentation/gold/5_1/gold/gold.1.68.html#245104
> )?
>
> Q3. Does it make reliable convertion from pdb ro mol2 or it is better to
> make some changes by hands in mol2 and then import it?
>
> Q4. What degree of accuracy this soft can provide? And, especially, what
> about biological molecule (derivatives) like ATP, modified amino acids?
> As I know swissparam.ch developed for charmm27 had some problem with it.
>
> Q5. As I'm working with amber forcefield bith in gromacs4.5.5 and amber11
> I'm using AM1 bcc flag. So what about the string, is it correct?
>
>
> antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc -s 2
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Received on Tue Oct 30 2012 - 02:00:04 PDT
